Commit 1c905c2c authored by RomainFeron's avatar RomainFeron
Browse files

Added license notice headers

parent 9edc859f
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include <iostream>
#include <stdio.h>
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "depth.h"
#include <iostream>
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include <algorithm>
#include <fstream>
......@@ -5,7 +23,7 @@
#include <string>
#include <unordered_map>
#include <vector>
#include "depth_table.h"
#include "table_parser.h"
#include "parameters.h"
#include "popmap.h"
#include "utils.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "distrib.h"
void distrib(Parameters& parameters) {
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include <fstream>
#include <string>
#include <unordered_map>
#include <vector>
#include "depth_table.h"
#include "table_parser.h"
#include "stats.h"
#include "parameters.h"
#include "popmap.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "freq.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include <fstream>
#include <string>
#include <unordered_map>
#include <vector>
#include "depth_table.h"
#include "table_parser.h"
#include "parameters.h"
#include "popmap.h"
#include "utils.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "arg_parser.h"
#include "depth.h"
#include "distrib.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "map.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include <fstream>
#include <string>
......@@ -5,7 +23,7 @@
#include <vector>
#include "bwa/bwamem.h"
#include "bwa/kseq.h"
#include "depth_table.h"
#include "table_parser.h"
#include "parameters.h"
#include "popmap.h"
#include "stats.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include <string>
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "popmap.h"
Popmap load_popmap(Parameters& parameters, bool compare) {
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include <unordered_map>
#include "parameters.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "process.h"
KSEQ_INIT(gzFile, gzread) // Kseq init macro
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include <dirent.h>
#include <iostream>
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "signif.h"
void signif(Parameters& parameters) {
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include <fstream>
#include <string>
#include <unordered_map>
#include <vector>
#include "depth_table.h"
#include "table_parser.h"
#include "parameters.h"
#include "popmap.h"
#include "stats.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "stats.h"
double get_chi_squared_p(double chi_squared) {
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#pragma once
#include "kfun/kfun.h"
#include "utils.h"
......
/*
* Copyright (C) 2020 Romain Feron
* This file is part of RADSex.
* RADSex is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
* RADSex is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with RADSex. If not, see <https://www.gnu.org/licenses/>.
*/
#include "subset.h"
void subset(Parameters& parameters) {
......
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